Bones not animated on mecanim?

I believe I got this to work in the past by checking Keep Additional Bones on the Rig import panel. But, just like with legacy, the animation needs to exactly match the additional bones. They're not retargetable.

Sorry, I'm not near Unity at the moment to double-check that, but I wanted to post an answer to share how I'm handling it right now. I control facial/lip sync animation using the legacy system (Animation component) and body animation using mecanim (Animator component) on the same character, and it works fine. Your legacy animation should only animate bones that are not controlled by your avatar.